Studies on Nonfruiting Myxobacteria: I. Cytophaga johnsonae , n.sp., a Chitin-decomposing Myxobacterium

From Nature-Sourced Polysaccharide Particles to Advanced Functional Materials

Polysaccharides constitute over 90% of the carbohydrate mass in nature, which makes them a promising feedstock for manufacturing sustainable materials. Polysaccharide particles (PSPs) are used as effective scavengers, carriers of chemical and biological cargos, and building blocks for the fabrication of macroscopic materials. The biocompatibility and degradability of PSPs are advantageous for their uses as biomaterials with more environmental friendliness. This review highlights the progresses in PSP applications as advanced functional materials, by describing PSP extraction, preparation, and surface functionalization with a variety of functional groups, polymers, nanoparticles, and biologically active species. This review also outlines the fabrication of PSP-derived macroscopic materials, as well as their applications in soft robotics, sensing, scavenging, water harvesting, drug delivery, and bioengineering. The paper is concluded with an outlook providing perspectives in the development and applications of PSP-derived materials.

Analysis of Culturable Bacterial Diversity of Pangong Tso Lake via a 16S rRNA Tag Sequencing Approach

The Pangong Tso lake is a high-altitude freshwater habitat wherein the resident microbes experience unique selective pressures, i.e., high radiation, low nutrient content, desiccation, and temperature extremes. Our study attempts to analyze the diversity of culturable bacteria by applying a high-throughput amplicon sequencing approach based on long read technology to determine the spectrum of bacterial diversity supported by axenic media. The phyla Pseudomonadota, Bacteriodetes, and Actinomycetota were retrieved as the predominant taxa in both water and sediment samples. The genera Hydrogenophaga and Rheinheimera, Pseudomonas, Loktanella, Marinomonas, and Flavobacterium were abundantly present in the sediment and water samples, respectively. Low nutrient conditions supported the growth of taxa within the phyla Bacteriodetes, Actinomycetota, and Cyanobacteria and were biased towards the selection of Pseudomonas, Hydrogenophaga, Bacillus, and Enterococcus spp. Our study recommends that media formulations can be finalized after analyzing culturable diversity through a high-throughput sequencing effort to retrieve maximum species diversity targeting novel/relevant taxa.

The gender gap in names of prokaryotes honouring persons

The aim of this study is to analyse prokaryotic names which honour persons, eponyms, from a gender perspective. Data were retrieved from the List of Prokaryotic names with Standing in Nomenclature. Excluding new combinations, the etymologies of 23 315 unique names at the rank of genus, species and subspecies were analysed. A total of 2018 (8.7 %) names honour persons (eponyms), for which the development of the female share over time was further investigated. Women started to be honoured very recently (1947) compared to men (1823). Moreover, only 14.8 % of all prokaryotic eponyms refer to females. This ratio has hardly improved since 1947, although the number of women whose contributions to microbiology could have been recognized has increased over time. In contrast, about 50 % of prokaryotic names derived from mythological characters refer to females. To reduce this gender gap, we encourage authors proposing new taxon names to honour female scientists who can serve as role models for new generations.

Bacteroidota polysaccharide utilization system for branched dextran exopolysaccharides from lactic acid bacteria

Dextran is an α-(1→6)-glucan that is synthesized by some lactic acid bacteria, and branched dextran with α-(1→2)-, α-(1→3)-, and α-(1→4)-linkages are often produced. Although many dextranases are known to act on the α-(1→6)-linkage of dextran, few studies have functionally analyzed the proteins involved in degrading branched dextran. The mechanism by which bacteria utilize branched dextran is unknown. Earlier, we identified dextranase (FjDex31A) and kojibiose hydrolase (FjGH65A) in the dextran utilization locus (FjDexUL) of a soil Bacteroidota Flavobacterium johnsoniae and hypothesized that FjDexUL is involved in the degradation of α-(1→2)-branched dextran. In this study, we demonstrate that FjDexUL proteins recognize and degrade α-(1→2)- and α-(1→3)-branched dextrans produced by Leuconostoc citreum S-32 (S-32 α-glucan). The FjDexUL gene was significantly upregulated when S-32 α-glucan was the carbon source compared with α-glucooligosaccharides and α-glucans, such as linear dextran and branched α-glucan from L. citreum S-64. FjDexUL GHs synergistically degraded S-32 α-glucan. The crystal structure of FjGH66 shows that some sugar-binding subsites can accommodate α-(1→2)- and α-(1→3)-branches. The structure of FjGH65A in complex with isomaltose supports that FjGH65A acts on α-(1→2)-glucosyl isomaltooligosaccharides. Furthermore, two cell surface sugar-binding proteins (FjDusD and FjDusE) were characterized, and FjDusD showed affinity for isomaltooligosaccharides and FjDusE for dextran, including linear and branched dextrans. Collectively, FjDexUL proteins are suggested to be involved in the degradation of α-(1→2)- and α-(1→3)-branched dextrans. Our results will be helpful in understanding the bacterial nutrient requirements and symbiotic relationships between bacteria at the molecular level.

Transposon mutagenesis and genome sequencing identify two novel, tandem genes involved in the colony spreading of Flavobacterium collinsii, isolated from an ayu fish, Plecoglossus altivelis

Bacteria of the family Flavobacteriaceae (flavobacteria) primarily comprise nonpathogenic bacteria that inhabit soil and water (both marine and freshwater). However, some bacterial species in the family, including Flavobacterium psychrophilum and Flavobacterium columnare, are known to be pathogenic to fish. Flavobacteria, including the abovementioned pathogenic bacteria, belong to the phylum Bacteroidota and possess two phylum-specific features, gliding motility and a protein secretion system, which are energized by a common motor complex. Herein, we focused on Flavobacterium collinsii (GiFuPREF103) isolated from a diseased fish (Plecoglossus altivelis). Genomic analysis of F. collinsii GiFuPREF103 revealed the presence of a type IX secretion system and additional genes associated with gliding motility and spreading. Using transposon mutagenesis, we isolated two mutants with altered colony morphology and colony spreading ability; these mutants had transposon insertions in pep25 and lbp26. The glycosylation material profiles revealed that these mutants lacked the high-molecular-weight glycosylated materials present in the wild-type strain. In addition, the wild-type strains exhibited fast cell population movement at the edge of the spreading colony, whereas reduced cell population behavior was observed in the pep25- and lbp26-mutant strains. In the aqueous environment, the surface layers of these mutant strains were more hydrophobic, and they formed biofilms with enhanced microcolony growth compared to those with the wild-type. In Flavobacterium johnsoniae, the Fjoh_0352 and Fjoh_0353 mutant strains were generated, which were based on the ortholog genes of pep25 and lbp26. In these F. johnsoniae mutants, as in F. collinsii GiFuPREF103, colonies with diminished spreading capacity were formed. Furthermore, cell population migration was observed at the edge of the colony in wild-type F. johnsoniae, whereas individual cells, and not cell populations, migrated in these mutant strains. The findings of the present study indicate that pep25 and lbp26 contribute to the colony spreading of F. collinsii.

Identification of the Flavobacterium johnsoniae cysteate-fatty acyl transferase required for capnine synthesis and for efficient gliding motility

Sulfonolipids (SLs) are bacterial lipids that are structurally related to sphingolipids. Synthesis of this group of lipids seems to be mainly restricted to Flavobacterium, Cytophaga and other members of the phylum Bacteroidetes. These lipids have a wide range of biological activities: they can induce multicellularity in choanoflagellates, act as von Willebrand factor receptor antagonists, inhibit DNA polymerase, or function as tumour suppressing agents. In Flavobacterium johnsoniae, their presence seems to be required for efficient gliding motility. Until now, no genes/enzymes involved in SL synthesis have been identified, which has been limiting for the study of some of the biological effects these lipids have. Here, we describe the identification of the cysteate-fatty acyl transferase Fjoh_2419 required for synthesis of the SL precursor capnine in F. johnsoniae. This enzyme belongs to the α-oxoamine synthase family similar to serine palmitoyl transferases, 2-amino-3-oxobutyrate coenzyme A ligase and 8-amino-7-oxononanoate synthases. Expression of the gene fjoh_2419 in Escherichia coli caused the formation of a capnine-derived molecule. Flavobacterium johnsoniae mutants deficient in fjoh_2419 lacked SLs and were more sensitive to many antibiotics. Mutant growth was not affected in liquid medium but the cells exhibited defects in gliding motility.

Identification of a major glucose transporter in Flavobacterium johnsoniae: Inhibition of F. johnsoniae colony spreading by glucose uptake

Many members of the phylum Bacteroidetes, such as Flavobacterium johnsoniae, can glide over a solid surface: an ability called gliding motility. It can be usually observed on agar plates as thin, flat, spreading colonies with irregular, feathery edges; this phenomenon is called colony spreading. Colony spreading of F. johnsoniae on 1.5% agar plates containing poor nutrients is dose-dependently inhibited by addition of D-glucose, as previously reported. Accordingly, here, we created mutants (by transposon mutagenesis) that partially suppressed glucose-mediated inhibition of colony spreading. Among the isolates, we found that one had a transposon insertion in Fjoh_4565, tentatively named mfsA, which encodes a major facilitator superfamily (MFS) transporter previously shown to be required for growth on glucose, N-acetyl-glucosamine, and chitin. We constructed an mfsA deletion mutant and found that the mutant showed no glucose-mediated acceleration of growth or glucose uptake. The mfsA gene complemented the phenotype of a glucose-negative Escherichia coli. These results suggest that the mfsA gene encodes the sole MFS transporter of glucose in F. johnsoniae and that glucose uptake is partially required for the glucose-mediated inhibition of F. johnsoniae colony spreading.

Marine Myxobacteria: A Few Good Halophiles

Currently considered an excellent candidate source of novel chemical diversity, the existence of marine myxobacteria was in question less than 20 years ago. This review aims to serve as a roll call for marine myxobacteria and to summarize their unique features when compared to better-known terrestrial myxobacteria. Characteristics for discrimination between obligate halophilic, marine myxobacteria and halotolerant, terrestrial myxobacteria are discussed. The review concludes by highlighting the need for continued discovery and exploration of marine myxobacteria as producers of novel natural products.

The Type IX Secretion System (T9SS): Highlights and Recent Insights into Its Structure and Function

Protein secretion systems are vital for prokaryotic life, as they enable bacteria to acquire nutrients, communicate with other species, defend against biological and chemical agents, and facilitate disease through the delivery of virulence factors. In this review, we will focus on the recently discovered type IX secretion system (T9SS), a complex translocon found only in some species of the Bacteroidetes phylum. T9SS plays two roles, depending on the lifestyle of the bacteria. It provides either a means of movement (called gliding motility) for peace-loving environmental bacteria or a weapon for pathogens. The best-studied members of these two groups are Flavobacterium johnsoniae, a commensal microorganism often found in water and soil, and Porphyromonas gingivalis, a human oral pathogen that is a major causative agent of periodontitis. In P. gingivalis and some other periodontopathogens, T9SS translocates proteins, especially virulence factors, across the outer membrane (OM). Proteins destined for secretion bear a conserved C-terminal domain (CTD) that directs the cargo to the OM translocon. At least 18 proteins are involved in this still enigmatic process, with some engaged in the post-translational modification of T9SS cargo proteins. Upon translocation across the OM, the CTD is removed by a protease with sortase-like activity and an anionic LPS is attached to the newly formed C-terminus. As a result, a cargo protein could be secreted into the extracellular milieu or covalently attached to the bacterial surface. T9SS is regulated by a two-component system; however, the precise environmental signal that triggers it has not been identified. Exploring unknown systems contributing to bacterial virulence is exciting, as it may eventually lead to new therapeutic strategies. During the past decade, the major components of T9SS were identified, as well as hints suggesting the possible mechanism of action. In addition, the list of characterized cargo proteins is constantly growing. The actual structure of the translocon, situated in the OM of bacteria, remains the least explored area; however, new technical approaches and increasing scientific attention have resulted in a growing body of data. Therefore, we present a compact up-to-date review of this topic.

The Type IX Secretion System (T9SS): Highlights and Recent Insights into Its Structure and Function

Protein secretion systems are vital for prokaryotic life, as they enable bacteria to acquire nutrients, communicate with other species, defend against biological and chemical agents, and facilitate disease through the delivery of virulence factors. In this review, we will focus on the recently discovered type IX secretion system (T9SS), a complex translocon found only in some species of the Bacteroidetes phylum. T9SS plays two roles, depending on the lifestyle of the bacteria. It provides either a means of movement (called gliding motility) for peace-loving environmental bacteria or a weapon for pathogens. The best-studied members of these two groups are Flavobacterium johnsoniae, a commensal microorganism often found in water and soil, and Porphyromonas gingivalis, a human oral pathogen that is a major causative agent of periodontitis. In P. gingivalis and some other periodontopathogens, T9SS translocates proteins, especially virulence factors, across the outer membrane (OM). Proteins destined for secretion bear a conserved C-terminal domain (CTD) that directs the cargo to the OM translocon. At least 18 proteins are involved in this still enigmatic process, with some engaged in the post-translational modification of T9SS cargo proteins. Upon translocation across the OM, the CTD is removed by a protease with sortase-like activity and an anionic LPS is attached to the newly formed C-terminus. As a result, a cargo protein could be secreted into the extracellular milieu or covalently attached to the bacterial surface. T9SS is regulated by a two-component system; however, the precise environmental signal that triggers it has not been identified. Exploring unknown systems contributing to bacterial virulence is exciting, as it may eventually lead to new therapeutic strategies. During the past decade, the major components of T9SS were identified, as well as hints suggesting the possible mechanism of action. In addition, the list of characterized cargo proteins is constantly growing. The actual structure of the translocon, situated in the OM of bacteria, remains the least explored area; however, new technical approaches and increasing scientific attention have resulted in a growing body of data. Therefore, we present a compact up-to-date review of this topic.

Draft Genome Sequence of Flavobacterium johnsoniae CI04, an Isolate from the Soybean Rhizosphere

Flavobacterium johnsoniae CI04 was coisolated with Bacillus cereus from a root of a field-grown soybean plant in Arlington, WI, and selected as a model for studying commensalism between members of the Cytophaga-Flavobacterium-Bacteroides group and B. cereus. Here we report the draft genome sequence of F. johnsoniae CI04 obtained by Illumina sequencing.

High-quality draft genome sequence of Flavobacterium suncheonense GH29-5(T) (DSM 17707(T)) isolated from greenhouse soil in South Korea, and emended description of Flavobacterium suncheonense GH29-5(T)

Flavobacterium suncheonense is a member of the family Flavobacteriaceae in the phylum Bacteroidetes. Strain GH29-5^T (DSM 17707^T) was isolated from greenhouse soil in Suncheon, South Korea. F. suncheonense GH29-5^T is part of the GenomicEncyclopedia ofBacteria andArchaea project. The 2,880,663 bp long draft genome consists of 54 scaffolds with 2739 protein-coding genes and 82 RNA genes. The genome of strain GH29-5^T has 117 genes encoding peptidases but a small number of genes encoding carbohydrate active enzymes (51 CAZymes). Metallo and serine peptidases were found most frequently. Among CAZymes, eight glycoside hydrolase families, nine glycosyl transferase families, two carbohydrate binding module families and four carbohydrate esterase families were identified. Suprisingly, polysaccharides utilization loci (PULs) were not found in strain GH29-5^T. Based on the coherent physiological and genomic characteristics we suggest that F. suncheonense GH29-5^T feeds rather on proteins than saccharides and lipids.

Metagenomic analysis of the Rhinopithecus bieti fecal microbiome reveals a broad diversity of bacterial and glycoside hydrolase profiles related to lignocellulose degradation

BACKGROUND

The animal gastrointestinal tract contains a complex community of microbes, whose composition ultimately reflects the co-evolution of microorganisms with their animal host and the diet adopted by the host. Although the importance of gut microbiota of humans has been well demonstrated, there is a paucity of research regarding non-human primates (NHPs), especially herbivorous NHPs.

RESULTS

In this study, an analysis of 97,942 pyrosequencing reads generated from Rhinopithecus bieti fecal DNA extracts was performed to help better understanding of the microbial diversity and functional capacity of the R. bieti gut microbiome. The taxonomic analysis of the metagenomic reads indicated that R. bieti fecal microbiomes were dominated by Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria phyla. The comparative analysis of taxonomic classification revealed that the metagenome of R. bieti was characterized by an overrepresentation of bacteria of phylum Fibrobacteres and Spirochaetes as compared with other animals. Primary functional categories were associated mainly with protein, carbohydrates, amino acids, DNA and RNA metabolism, cofactors, cell wall and capsule and membrane transport. Comparing glycoside hydrolase profiles of R. bieti with those of other animal revealed that the R. bieti microbiome was most closely related to cow rumen.

CONCLUSIONS

Metagenomic and functional analysis demonstrated that R. bieti possesses a broad diversity of bacteria and numerous glycoside hydrolases responsible for lignocellulosic biomass degradation which might reflect the adaptations associated with a diet rich in fibrous matter. These results would contribute to the limited body of NHPs metagenome studies and provide a unique genetic resource of plant cell wall degrading microbial enzymes. However, future studies on the metagenome sequencing of R. bieti regarding the effects of age, genetics, diet and environment on the composition and activity of the metagenomes are required.

Flavobacterium johnsoniae chitinase ChiA is required for chitin utilization and is secreted by the type IX secretion system

Flavobacterium johnsoniae, a member of phylum Bacteriodetes, is a gliding bacterium that digests insoluble chitin and many other polysaccharides. A novel protein secretion system, the type IX secretion system (T9SS), is required for gliding motility and for chitin utilization. Five potential chitinases were identified by genome analysis. Fjoh_4555 (ChiA), a 168.9-kDa protein with two glycoside hydrolase family 18 (GH18) domains, was targeted for analysis. Disruption of chiA by insertional mutagenesis resulted in cells that failed to digest chitin, and complementation with wild-type chiA on a plasmid restored chitin utilization. Antiserum raised against recombinant ChiA was used to detect the protein and to characterize its secretion by F. johnsoniae. ChiA was secreted in soluble form by wild-type cells but remained cell associated in strains carrying mutations in any of the T9SS genes, gldK, gldL, gldM, gldNO, sprA, sprE, and sprT. Western blot and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analyses suggested that ChiA was proteolytically processed into two GH18 domain-containing proteins. Proteins secreted by T9SSs typically have conserved carboxy-terminal domains (CTDs) belonging to the TIGRFAM families TIGR04131 and TIGR04183. ChiA does not exhibit strong similarity to these sequences and instead has a novel CTD. Deletion of this CTD resulted in accumulation of ChiA inside cells. Fusion of the ChiA CTD to recombinant mCherry resulted in secretion of mCherry into the medium. The results indicate that ChiA is a soluble extracellular chitinase required for chitin utilization and that it relies on a novel CTD for secretion by the F. johnsoniae T9SS.

Flavobacterium johnsoniae GldK, GldL, GldM, and SprA are required for secretion of the cell surface gliding motility adhesins SprB and RemA

Flavobacterium johnsoniae cells move rapidly over surfaces by gliding motility. Gliding results from the movement of adhesins such as SprB and RemA along the cell surface. These adhesins are delivered to the cell surface by a Bacteroidetes-specific secretion system referred to as the type IX secretion system (T9SS). GldN, SprE, SprF, and SprT are involved in secretion by this system. Here we demonstrate that GldK, GldL, GldM, and SprA are each also involved in secretion. Nonpolar deletions of gldK, gldL, or gldM resulted in the absence of gliding motility and in T9SS defects. The mutant cells produced SprB and RemA proteins but failed to secrete them to the cell surface. The mutants were resistant to phages that use SprB or RemA as a receptor, and they failed to attach to glass, presumably because of the absence of cell surface adhesins. Deletion of sprA resulted in similar but slightly less dramatic phenotypes. sprA mutant cells failed to secrete SprB and RemA, but cells remained susceptible to some phages and retained some limited ability to glide. The phenotype of the sprA mutant was similar to those previously described for sprE and sprT mutants. SprA, SprE, and SprT are needed for secretion of SprB and RemA but may not be needed for secretion of other proteins targeted to the T9SS. Genetic and molecular experiments demonstrate that gldK, gldL, gldM, and gldN form an operon and suggest that the proteins encoded by these genes may interact to form part of the F. johnsoniae T9SS.

Plastome Sequence Determination and Comparative Analysis for Members of the Lolium-Festuca Grass Species Complex

Chloroplast genome sequences are of broad significance in plant biology, due to frequent use in molecular phylogenetics, comparative genomics, population genetics, and genetic modification studies. The present study used a second-generation sequencing approach to determine and assemble the plastid genomes (plastomes) of four representatives from the agriculturally important Lolium-Festuca species complex of pasture grasses (Lolium multiflorum, Festuca pratensis, Festuca altissima, and Festuca ovina). Total cellular DNA was extracted from either roots or leaves, was sequenced, and the output was filtered for plastome-related reads. A comparison between sources revealed fewer plastome-related reads from root-derived template but an increase in incidental bacterium-derived sequences. Plastome assembly and annotation indicated high levels of sequence identity and a conserved organization and gene content between species. However, frequent deletions within the F. ovina plastome appeared to contribute to a smaller plastid genome size. Comparative analysis with complete plastome sequences from other members of the Poaceae confirmed conservation of most grass-specific features. Detailed analysis of the rbcL-psaI intergenic region, however, revealed a "hot-spot" of variation characterized by independent deletion events. The evolutionary implications of this observation are discussed. The complete plastome sequences are anticipated to provide the basis for potential organelle-specific genetic modification of pasture grasses.

Flavobacterium tilapiae sp. nov., isolated from a freshwater pond, and emended descriptions of Flavobacterium defluvii and Flavobacterium johnsoniae

A bacterial strain, designated Ruye-71T, was isolated from a freshwater tilapiine cichlid fish culture pond in Taiwan and characterized in a taxonomic study using a polyphasic approach. Cells of strain Ruye-71T were Gram-stain-negative, strictly aerobic, yellow-pigmented rods that were motile by gliding. Growth occurred at 10–30 °C (optimum, 15–30 °C), at pH 7.0–8.0 (optimum, pH 8.0) and with 0–2 % NaCl (optimum, 0–1 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Ruye-71T belonged to the genus Flavobacterium and was most closely related to Flavobacterium defluvii EMB117T, with a 16S rRNA gene sequence similarity of 97.7 %. Strain Ruye-71T contained iso-C15 : 0, summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c), C16 : 0, C16 : 0 3-OH, iso-C15 : 0 3-OH and iso-C17 : 0 3-OH as major fatty acids. The major isoprenoid quinone was MK-6. The polar lipid profile consisted of phosphatidylethanolamine and several unidentified polar lipids. The DNA G+C content of the genomic DNA of strain Ruye-71T was 39.2 mol%. The mean level of DNA–DNA relatedness between strain Ruye-71T and Flavobacterium defluvii DSM 17963T was 39.9±1.2 %. On the basis of phylogenetic inference and phenotypic data, strain Ruye-71T should be classified as representing a novel species, for which the name Flavobacterium tilapiae sp. nov. is proposed. The type strain is Ruye-71T ( = BCRC 80262T = KCTC 23312T). Emended descriptions of Flavobacterium defluvii and Flavobacterium johnsoniae are also proposed.

Glitter-like iridescence within the bacteroidetes especially Cellulophaga spp.: optical properties and correlation with gliding motility

Iridescence results from structures that generate color. Iridescence of bacterial colonies has recently been described and illustrated. The glitter-like iridescence class, created especially for a few strains of Cellulophaga lytica, exhibits an intense iridescence under direct illumination. Such color appearance effects were previously associated with other bacteria from the Bacteroidetes phylum, but without clear elucidation and illustration. To this end, we compared various bacterial strains to which the iridescent trait was attributed. All Cellulophaga species and additional Bacteroidetes strains from marine and terrestrial environments were investigated. A selection of bacteria, mostly marine in origin, were found to be iridescent. Although a common pattern of reflected wavelengths was recorded for the species investigated, optical spectroscopy and physical measurements revealed a range of different glitter-like iridescence intensity and color profiles. Importantly, gliding motility was found to be a common feature of all iridescent colonies. Dynamic analyses of “glitter” formation at the edges of C. lytica colonies showed that iridescence was correlated with layer superposition. Both gliding motility, and unknown cell-to-cell communication processes, may be required for the establishment, in time and space, of the necessary periodic structures responsible for the iridescent appearance of Bacteroidetes.

Flavobacterium compostarboris sp. nov., isolated from leaf-and-branch compost, and emended descriptions of Flavobacterium hercynium , Flavobacterium resistens and Flavobacterium johnsoniae

A strictly aerobic, Gram-negative, yellow-pigmented, non-spore-forming rod, designated 15C3T, was isolated from aerobic leaf-and-branch compost at EXPO Park in Osaka, Japan. Growth was observed at 9–33 °C (optimum 25 °C) and pH 5.6–7.9 (optimum pH 6.1–7.0). No growth occurred with >2 % (w/v) NaCl. Strain 15C3T reduced nitrate to nitrogen and showed catalase activity but not oxidase activity. The predominant fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH). The isolate contained phosphatidylethanolamine as the major polar lipid and menaquinone-6 as the major respiratory quinone. The G+C content of the genomic DNA of strain 15C3T was 33.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 15C3T belonged to the genus Flavobacterium and was most closely related to Flavobacterium hercynium WB 4.2-33T (96.9 % sequence similarity). On the basis of phenotypic and phylogenetic distinctiveness, strain 15C3T is considered to represent a novel species in the genus Flavobacterium , for which the name Flavobacterium compostarboris sp. nov. is proposed. The type strain is 15C3T ( = KACC 14224T  = JCM 16527T). Emended descriptions of F. hercynium , Flavobacterium resistens and Flavobacterium johnsoniae are also given.

Flavobacterium chungbukense sp. nov., isolated from soil

A yellow-pigmented, Gram-staining-negative, non-motile, strictly aerobic and rod-shaped bacterium, designated CS100T, was isolated from soil in Chungbuk, Korea. Phylogenetic analysis and comparative studies based on the 16S rRNA gene sequence showed that strain CS100T belonged to the genus Flavobacterium in the family Flavobacteriaceae. Strain CS100T showed the highest sequence similarities to Flavobacterium glaciei JCM 13953T (97.6 %) and Flavobacterium johnsoniae KACC 11410T (97.1 %). Sequence similarity to other members of the genus Flavobacterium was 91.5–97.0 %. Growth occurred at 4–30 °C, at pH 5.0–9.0 and in the presence of 0–2 % (w/v) NaCl. Flexirubin-type pigments were produced. Menaquinone-6 (MK-6) was the major respiratory quinone and the major fatty acids were iso-C15 : 0 (17.3 %), summed feature 3 (comprising iso-C15 : 0 2-OH and/or C16 : 1ω7c, 15.5 %) and C16 : 0 (11.8 %). The DNA G+C content was 36.4 mol%. Strain CS100T hydrolysed skimmed milk and gelatin, but not chitin or pectin, and showed oxidase and catalase activities. DNA–DNA relatedness was 3.0 % with F. glaciei JCM 13953T and 11.5 % with F. johnsoniae KACC 11410T. On the basis of the evidence from this study, strain CS100T represents a novel species of the genus Flavobacterium, for which the name Flavobacterium chungbukense sp. nov. is proposed. The type strain is CS100T ( = KACC 15048T = JCM 17386T).

Flavobacterium johnsoniae gldN and gldO are partially redundant genes required for gliding motility and surface localization of SprB

Cells of the gliding bacterium Flavobacterium johnsoniae move rapidly over surfaces. Mutations in gldN cause a partial defect in gliding. A novel bacteriophage selection strategy was used to aid construction of a strain with a deletion spanning gldN and the closely related gene gldO in an otherwise wild-type F. johnsoniae UW101 background. Bacteriophage transduction was used to move a gldN mutation into F. johnsoniae UW101 to allow phenotypic comparison with the gldNO deletion mutant. Cells of the gldN mutant formed nonspreading colonies on agar but retained some ability to glide in wet mounts. In contrast, cells of the gldNO deletion mutant were completely nonmotile, indicating that cells require GldN, or the GldN-like protein GldO, to glide. Recent results suggest that Porphyromonas gingivalis PorN, which is similar in sequence to GldN, has a role in protein secretion across the outer membrane. Cells of the F. johnsoniae gldNO deletion mutant were defective in localization of the motility protein SprB to the cell surface, suggesting that GldN may be involved in secretion of components of the motility machinery. Cells of the gldNO deletion mutant were also deficient in chitin utilization and were resistant to infection by bacteriophages, phenotypes that may also be related to defects in protein secretion.

Novel features of the polysaccharide-digesting gliding bacterium Flavobacterium johnsoniae as revealed by genome sequence analysis

The 6.10-Mb genome sequence of the aerobic chitin-digesting gliding bacterium Flavobacterium johnsoniae (phylum Bacteroidetes) is presented. F. johnsoniae is a model organism for studies of bacteroidete gliding motility, gene regulation, and biochemistry. The mechanism of F. johnsoniae gliding is novel, and genome analysis confirms that it does not involve well-studied motility organelles, such as flagella or type IV pili. The motility machinery is composed of Gld proteins in the cell envelope that are thought to comprise the "motor" and SprB, which is thought to function as a cell surface adhesin that is propelled by the motor. Analysis of the genome identified genes related to sprB that may encode alternative adhesins used for movement over different surfaces. Comparative genome analysis revealed that some of the gld and spr genes are found in nongliding bacteroidetes and may encode components of a novel protein secretion system. F. johnsoniae digests proteins, and 125 predicted peptidases were identified. F. johnsoniae also digests numerous polysaccharides, and 138 glycoside hydrolases, 9 polysaccharide lyases, and 17 carbohydrate esterases were predicted. The unexpected ability of F. johnsoniae to digest hemicelluloses, such as xylans, mannans, and xyloglucans, was predicted based on the genome analysis and confirmed experimentally. Numerous predicted cell surface proteins related to Bacteroides thetaiotaomicron SusC and SusD, which are likely involved in binding of oligosaccharides and transport across the outer membrane, were also identified. Genes required for synthesis of the novel outer membrane flexirubin pigments were identified by a combination of genome analysis and genetic experiments. Genes predicted to encode components of a multienzyme nonribosomal peptide synthetase were identified, as were novel aspects of gene regulation. The availability of techniques for genetic manipulation allows rapid exploration of the features identified for the polysaccharide-digesting gliding bacteroidete F. johnsoniae.

The convergence of carbohydrate active gene repertoires in human gut microbes

The extreme variation in gene content among phylogenetically related microorganisms suggests that gene acquisition, expansion, and loss are important evolutionary forces for adaptation to new environments. Accordingly, phylogenetically disparate organisms that share a habitat may converge in gene content as they adapt to confront shared challenges. This response should be especially pronounced for functional genes that are important for survival in a particular habitat. We illustrate this principle by showing that the repertoires of two different types of carbohydrate-active enzymes, glycoside hydrolases and glycosyltransferases, have converged in bacteria and archaea that live in the human gut and that this convergence is largely due to horizontal gene transfer rather than gene family expansion. We also identify gut microbes that may have more similar dietary niches in the human gut than would be expected based on phylogeny. The techniques used to obtain these results should be broadly applicable to understanding the functional genes and evolutionary processes important for adaptation in many environments and useful for interpreting the large number of reference microbial genome sequences being generated for the International Human Microbiome Project.

SprB is a cell surface component of the Flavobacterium johnsoniae gliding motility machinery

Cells of the gliding bacterium Flavobacterium johnsoniae move rapidly over surfaces by an unknown mechanism. Transposon insertions in sprB resulted in cells that were defective in gliding. SprB is a highly repetitive 669-kDa cell surface protein, and antibodies against SprB inhibited the motility of wild-type cells. Polystyrene microspheres coated with antibodies against SprB attached to and were rapidly propelled along the cell surface, suggesting that SprB is one of the outermost components of the motility machinery. The movement of SprB along the cell surface supports a model of gliding motility in which motors anchored to the cell wall rapidly propel cell surface adhesins.

Flavobacterium johnsoniae SprA is a cell surface protein involved in gliding motility

Flavobacterium johnsoniae cells glide rapidly over surfaces by an unknown mechanism. Transposon-induced sprA mutants formed nonspreading colonies on agar, and the cells examined in wet mounts were deficient in attachment to surfaces and were almost completely nonmotile. Exposure of intact cells to proteinase K cleaved the 270-kDa SprA into several large peptides, suggesting that it is partially exposed on the cell surface.

Flavobacterium defluvii sp. nov., isolated from activated sludge

A Gram-negative bacterium, designated strain EMB117T, was isolated from a municipal wastewater treatment plant and characterized by polyphasic taxonomy. The cells were non-spore-forming rods that showed gliding motility. Optimal growth occurred at 25–30 °C and pH 7.0–8.0. Strain EMB117T contained phosphatidylethanolamine as the predominant polar lipid, and the major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 0 3-OH and summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH). The G+C content of the genomic DNA was 33.5 mol% and the major isoprenoid quinone was MK-6. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain EMB117T belonged to the genus Flavobacterium and was most closely related to Flavobacterium johnsoniae DSM 425T (97.8 % sequence similarity). The DNA–DNA relatedness between strain EMB117T and F. johnsoniae ATCC 17061T was about 18 %. On the basis of the phenotypic, chemotaxonomic and molecular data, strain EMB117T represents a novel species within the genus Flavobacterium, for which the name Flavobacterium defluvii sp. nov. is proposed. The type strain is EMB117T (=KCTC 12612T=DSM 17963T).

Mutations in Flavobacterium johnsoniae secDF result in defects in gliding motility and chitin utilization

secDF mutants of Flavobacterium johnsoniae were deficient in gliding motility and chitin utilization. Cells of the mutants had reduced levels of GldJ protein, which is required for both processes. SecDF is similar to Escherichia coli SecD and SecF, which are involved in protein secretion.

Flavobacterium johnsoniae gliding motility genes identified by mariner mutagenesis

Cells of Flavobacterium johnsoniae glide rapidly over surfaces. The mechanism of F. johnsoniae gliding motility is not known. Eight gld genes required for gliding motility have been described. Disruption of any of these genes results in complete loss of gliding motility, deficiency in chitin utilization, and resistance to bacteriophages that infect wild-type cells. Two modified mariner transposons, HimarEm1 and HimarEm2, were constructed to allow the identification of additional motility genes. HimarEm1 and HimarEm2 each transposed in F. johnsoniae, and nonmotile mutants were identified and analyzed. Four novel motility genes, gldK, gldL, gldM, and gldN, were identified. GldK is similar in sequence to the lipoprotein GldJ, which is required for gliding. GldL, GldM, and GldN are not similar in sequence to proteins of known function. Cells with mutations in gldK, gldL, gldM, and gldN were defective in motility and chitin utilization and were resistant to bacteriophages that infect wild-type cells. Introduction of gldA, gldB, gldD, gldFG, gldH, gldI, and gldJ and the region spanning gldK, gldL, gldM, and gldN individually into 50 spontaneous and chemically induced nonmotile mutants restored motility to each of them, suggesting that few additional F. johnsoniae gld genes remain to be identified.

Flavobacterium johnsoniae GldJ is a lipoprotein that is required for gliding motility

Cells of Flavobacterium johnsoniae glide rapidly over surfaces by an unknown mechanism. Eight genes required for gliding motility have been described. Complementation of the nonmotile mutant UW102-48 identified another gene, gldJ, that is required for gliding. gldJ mutants formed nonspreading colonies, and individual cells were completely nonmotile. Like previously described nonmotile mutants, gldJ mutants were deficient in chitin utilization and were resistant to bacteriophages that infect wild-type cells. Cell fractionation and labeling studies with [(3)H]palmitate indicated that GldJ is a lipoprotein. Mutations in gldA, gldB, gldD, gldF, gldG, gldH, or gldI resulted in normal levels of gldJ transcript but decreased levels of GldJ protein. Expression of truncated GldJ protein in wild-type cells resulted in a severe motility defect. GldJ was found in regular bands that suggest the presence of a helical structure within the cell envelope.

GldI is a lipoprotein that is required for Flavobacterium johnsoniae gliding motility and chitin utilization

Cells of Flavobacterium johnsoniae glide rapidly over surfaces by an unknown mechanism. Seven genes (gldA, gldB, gldD, gldF, gldG, gldH, and ftsX) that are required for gliding motility have been described. Complementation of the nonmotile mutants UW102-41, UW102-85, and UW102-92 identified another gene, gldI, that is required for gliding motility. gldI mutants formed nonspreading colonies, and individual cells were completely nonmotile. They were also resistant to bacteriophages that infect wild-type cells, and they failed to digest chitin. Introduction of wild-type gldI on a plasmid restored colony spreading, cell motility, phage sensitivity, and the ability to digest chitin to the gldI mutants. gldI encodes a predicted 199-amino-acid protein that localized to the membrane fraction. Labeling studies with [(3)H]palmitate indicated that GldI is a lipoprotein. GldI is similar to peptidyl-prolyl cis/trans-isomerases of the FK506-binding protein family and may be involved in folding cell envelope protein components of the motility machinery.

Flavobacterium johnsoniae GldH is a lipoprotein that is required for gliding motility and chitin utilization

Cells of Flavobacterium johnsoniae move rapidly over surfaces by gliding motility. The mechanism of this form of motility is not known. Six genes (gldA, gldB, gldD, gldF, gldG, and ftsX) that are required for gliding have been described. Tn4351 mutagenesis was used to identify another gene, gldH, which is required for cell movement. GldH mutants formed nonspreading colonies, and individual cells lacked the cell movements and ability to propel latex spheres along their surfaces that are characteristic of wild-type cells. gldH mutants also failed to digest chitin and were resistant to bacteriophages that infect wild-type cells. Introduction of pMM293, which carries wild-type gldH, restored to the gldH mutants colony spreading, cell motility, the ability to move latex spheres, phage sensitivity, and the ability to digest chitin. gldH encodes a predicted 141-amino-acid protein that localized to the membrane fraction. Labeling studies with [3H]palmitate demonstrated that GldH is a lipoprotein. GldB and GldD, which were previously described, also appear to be lipoproteins. GldH does not exhibit significant amino acid similarity to proteins of known function in the databases. Putative homologs of gldH of unknown function are found in motile (Cytophaga hutchinsonii) and apparently nonmotile (Bacteroides thetaiotaomicron, Bacteroides fragilis, Tannerella forsythensis, Porphyromonas gingivalis, and Prevotella intermedia) members of the Cytophaga-Flavobacterium-Bacteroides group.

Phospholipids and a novel glycine-containing lipoamino acid in Cytophaga johnsonae Stanier strain C21

Two-dimensional thin-layer chromatography revealed that Cytophaga johnsonae contains at least 10 kinds of lipid, 2 of which are phospholipids, namely, phosphatidylethanolamine and phosphatidylcholine. One of the remaining lipids is a novel lipid that contains an amino acid. The structure of this unusual lipid (lipoamino acid) was resolved by chemical and physicochemical methods. The fatty acyl moiety of this lipid was diverse. The structure of the major molecular species of the lipid was determined as iso-3-hydroxy heptadecanoic acid, amide linked to glycine and esterified to isopentadecanoic acid. This type of glycine-containing lipid is a novel biological material which we have called cytolipin, basing this nomenclature on the genus of the bacterium. This is the first report of the lipid composition of C. johnsonae.

Effect of pH, temperature, and growth conditions on the adhesion of a gliding bacterium and three nongliding bacteria to polystyrene

The effect of growth rate, growth phase, pH, and temperature on the permanent adhesion of a glidingFlexibacter sp. and three nongliding bacteria,Pseudomonas fluorescens, Enterobacter cloacae, andChromobacterium sp., to polystyrene substrata was investigated. The permanent adhesion of the flexibacter appeared to be related to growth, as levels of adhesion increased with increased growth rate in continuous culture and declined rapidly with death phase in batch culture. With the three nongliding bacteria, there was no relationship between growth rate and levels of permanent adhesion. The permanent adhesion of the nongliding bacteria was maximum between pH 5.5 and pH 7 and between 20 and 30°C, whereas the adhesion of the flexibacter progressively decreased with increasing temperature and pH. The effect of different nutrient conditions on the gliding motility of the flexibacter across agar was also investigated. Gliding motility was inhibited by increased nutrient concentration and was affected by carbon source. Inhibition appeared to be related to the accumulation of a viscous exopolymer. It is proposed that the differences in the permanent adhesion of the gliding and nongliding bacteria may be related to their adaptation to different ecological niches.

Isolation and characterization of nonspreading mutants of the gliding bacterium Cytophaga johnsonae

Three approaches were taken to isolate a total of 153 nonspreading mutants derived from our laboratory strain of Cytophaga johnsonae, UW101, or from its auxotrophic derivative, UW10538. Characterization of 109 of these mutants led to their placement in five general categories: (i) motile, nonspreading (MNS) mutants whose cells are motile to various degrees but whose colonies fail to spread on agar gels under any conditions of incubation; (ii) conditional nonspreading (CNS) mutants with motile cells whose colonies require more moisture to spread on agar gels than do those of wild-type cells; (iii) filamentous conditional motility (FCM) mutants whose cells grow as nonmotile filaments or as motile cells with wild-type morphology, depending on conditions of incubation; (iv) short, tumbling, nonspreading (STN) mutants with short cells that tumble constantly; and (v) truly nonmotile (TNM) mutants whose cells never move and whose colonies never spread under any conditions tested. All TNM mutants exhibited a remarkable pleiotropy not seen in the other four classes of mutants: all were resistant to 39 phages to which wild-type cells are sensitive, and all were unable to digest chitin, which is digested by wild-type cells. The correlation between ability to move and phage sensitivity was strengthened further by showing that 150 additional TNM mutants derived from UW101 and 43 TNM mutants derived from 29 independent isolates of C. johnsonae were resistant to all phages to which their parents were sensitive. Furthermore, motile revertants of TNM mutants became phage sensitive, and temperature-sensitive mutants were motile and phage sensitive at 25 degrees C and nonmotile and phage resistant at 32 degrees C. Evidence supports the conclusion that any mutation rendering cells truly nonmotile invariably alters cell surface-associated properties such as phage sensitivity and chitin digestion merely as a consequence of changing a moving cell surface to a static surface.

Ecology and taxonomy of chitinoclasticCytophaga and related chitin-degrading bacteria isolated from an estuary

A total of 103 strains of estuarine, Chitinoclastic bacteria isolated from water, and sediment samples collected from the upper Chesapeake Bay, including 17 freshwater and 11 seawater isolates, were subjected to numerical taxonomy analysis. The isolates included 44 yellow-orange pigmented strains classified asCytophaga-like bacteria (CLB) of theCytophagaceae. Salt requirement of the strains ranged from tolerance to ≤1% NaCl to an absolute requirement for NaCl, with 1% NaCl satisfying this requirement. The largest phenon consisted of facultatively anaerobic, oligo-nitrophilic, and flexirubin pigment-producing freshwater and estuarine isolates, and included reference strains of bothCytophaga johnsonae Stanier andCytophaga aquatilis Strohl and Tait. Other phena, containing a smaller number of strains, comprised marine and estuarine isolates which did not produce flexirubin pigments, and required organic nitrogen for growth and for production of chitinolytic enzymes. Salt-requiring, flexirubin pigment-producing, chitin-degrading strains were, on occasion, isolated from estuarine samples and represented phena found in estuaries. Most of theCytophaga isolates, as well as chitin-degrading species not of the genusCytophaga that were isolated from Chesapeake Bay, clustered in phena representing previously described species of aerobic, zymogenic, chitinoclastic bacteria. When the frequency of occurrence of features related to environmental parameters, viz., pH, salinity, temperature range of growth, and growth on media lacking organic nitrogen, was calculated, ecological groupings of strains in the 2 major phena of CLB could be distinguished among the estuarine, chitin-degrading bacteria.

Evolution of bacterial denitrification and denitrifier diversity

Little is known about the role of nitrate in evolution of bacterial energy-generating mechanisms. Denitrifying bacteria are commonly regarded to have evolved from nitrate-respiring bacteria. Some researchers regard denitrification to be the precursor of aerobic respiration; others feel the opposite is true. Currently recognized denitrifying bacteria such as Hyphomicrobium, Paracoccus, Pseudomonas and Thiobacillus form a very diverse group. However, inadequate testing procedures and uncertain taxonomic identification of many isolates may have overstated the number of genera with species capable of denitrification. Nitrate reductases are structurally similar among denitrifying bacteria, but distinct from the enzymes in other nitrate-reducing organisms. Denitryfying bacteria have one of two types of nitrite reductase, either a copper-containing enzyme or an enzyme containing a cytochrome cd moiety. Both types are distinct from other nitrate reductases. Organisms capable of dissimilatory nitrate reduction are widely distributed among eubacterial groups defined by 16S ribosomal RNA phylogeny. Indeed, nitrate reduction is an almost universal property of actinomycetes and enteric organisms. However, denitrification is restricted to genera within the purple photosynthetic group. Denitrification within the genus Pseudomonas is distributed in accordance with DNA and RNA homology complexes. Denitrifiers seem to have evolved from a common ancestor within the purple photosynthetic bacterial group, but not from a nitrate-reducing organism such as those found today. Although denitrification seems to have arisen at the same time as aerobic respiration, the evolutionary relationship between the two cannot be determined at this time.

Influence of Temperature Adaptation on Glucose Metabolism in a Psychrotrophic Strain of Cytophaga johnsonae

Selective enrichment of yellow-orange-pigmented, gram-negative bacteria related to Cytophaga johnsonae from lake sediment was dependent on low temperatures (ca. 5°C). However, this temperature effect was abolished when excessive amounts of dissolved organic carbon (10 mM N -acetylglucosamine) were added. A psychrotrophic freshwater isolate of C. johnsonae was used to study the physiological versatility of this group. Exponential growth rates were found to be dependent on the temperature to which the cells used as the inocula were acclimated. Glucose incorporation and respiration were also dependent upon the acclimation temperature of the inocula. Patterns of 14 CO 2 evolution obtained from position-labeled [ 14 C]glucose indicated that glucose was predominantly metabolized via the Embden-Meyerhof-Parnas pathway, which, however, was greatly reduced at 25°C when the concentration of glucose was as low as 5 μM/liter. Transport, respiration, and incorporation of glucose (0.2- to 20,000-μM/liter concentrations) into macromolecular cellular compounds were characterized by multiple K m values which were a function of substrate concentration and temperature. It appeared possible that these multiple K m values reflected the changing participation of the Embden-Meyerhof-Parnas pathway in glucose metabolism. These results may provide a physiological explanation for the selective enrichment of psychrotrophic freshwater cytophagas. Moreover, they exhibit the limits of interpreting kinetic data based on conventional heterotrophic potential measurements, especially when some complications may arise from temperature and substrate adaptations of the more versatile members of the chemoorganotrophic microflora such as C. johnsonae.

The influence of changes in the environment on twitching motility

By examining medium composition and cultural conditions quantitatively it was possible to define conditions suitable to bring twitching motility about. Such conditions include the use of freshly poured, relatively thick and only slightly dried plates of a dilute medium in which the agar concentration is not too high. Incubation should take place in a humid atmosphere. In fact, everything points to the humidity as a factor of the utmost importance. Using strains of Acinetobacter calcoaceticus, it was found that a pH value of the medium adjusted to 9.0 enhances twitching motility. Spreading growth was not produced if agarose was applied instead of ordinary agars. Twitching motility was inhibited by a number of different chlorides, potassium nitrate, Tween 80 and sodium taurocholate. Possible interpretations of these observations are discussed.